Changeset 4723

Timestamp:

Jan 13, 2009, 9:20:26 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

References #1190: API and interface for creating biomaterial lists

All functionality should now be in place. It turned out that the one-step-down restriction wasn't neccesary since it was possible to link multiple steps together. In other words, it is now possible to generate a list with all labeled extracts that descend from the selected biosources. It also possible to move in the other direction, eg. from labeled extract to biosource.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/BioMaterialList.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/biomaterial/BioSourceToSampleTransformer.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/biomaterial/ExtractToLabeledExtractTransformer.java (added)
• src/core/net/sf/basedb/util/biomaterial/ExtractToSampleTransformer.java (added)
• src/core/net/sf/basedb/util/biomaterial/LabeledExtractToExtractTransformer.java (added)
• src/core/net/sf/basedb/util/biomaterial/ListUtil.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/biomaterial/PooledChildrenTransformer.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/biomaterial/PooledParentsTransformer.java (added)
• src/core/net/sf/basedb/util/biomaterial/SampleToBioSourceTransformer.java (added)
• src/core/net/sf/basedb/util/biomaterial/SampleToExtractTransformer.java (added)
• src/core/net/sf/basedb/util/collections/CollectionTransformer.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/collections/MultiStepCollectionTransformer.java (added)
• src/test/TestSample.java (modified) (1 diff)
• www/biomaterials/lists/edit_list.jsp (modified) (6 diffs)
• www/biomaterials/lists/index.jsp (modified) (3 diffs)

trunk/src/core/net/sf/basedb/core/BioMaterialList.java

@@ -37 +37 @@
 import net.sf.basedb.core.data.BioMaterialData;
 import net.sf.basedb.core.data.BioMaterialListData;
+import net.sf.basedb.util.biomaterial.ListUtil;
 
 /**
@@ -401 +402 @@
     member type of the list.
     @return An {@link ItemQuery} object
-    @throws BaseException If the query could not be created and configured.
+    @throws BaseException If the query could not be created and configured
+    @see ListUtil#getQuery(Item)
   */
   public ItemQuery<? extends BioMaterial> getAllBioMaterials()
     throws BaseException
   {
-    ItemQuery<? extends BioMaterial> query;
-    Item memberType = getMemberType();
-    if (memberType == Item.BIOSOURCE)
-    {
-      query = BioSource.getQuery();
-    }
-    else if (memberType == Item.SAMPLE)
-    {
-      query = Sample.getQuery();
-    }
-    else if (memberType == Item.EXTRACT)
-    {
-      query = Extract.getQuery();
-    }
-    else if (memberType == Item.LABELEDEXTRACT)
-    {
-      query = LabeledExtract.getQuery();
-    }
-    else
-    {
-      throw new AssertionError("Unsupported member type in list '" + 
-          getName() + "': " + memberType);
-    }
-    return query;
+    return ListUtil.getQuery(getMemberType());
   }
 

trunk/src/core/net/sf/basedb/util/biomaterial/BioSourceToSampleTransformer.java

@@ -23 +23 @@
 
 import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
 
 import net.sf.basedb.core.BioSource;
@@ -29 +31 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Sample;
+import net.sf.basedb.core.Type;
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Restrictions;
+import net.sf.basedb.util.collections.BasicItemToIdTransformer;
 import net.sf.basedb.util.collections.CollectionTransformer;
 
@@ -65 +69 @@
       Collection<? super Sample> samples)
   {
-    ItemQuery<Sample> query = Sample.getQuery();
-    query.include(Include.ALL);
+    // Copy source ID:s so we can use them as a parameter in the query
+    Set<Integer> sourceIds = new HashSet<Integer>();
+    BasicItemToIdTransformer idTransformer = new BasicItemToIdTransformer();
+    idTransformer.transform(bioSources, sourceIds);
+
+    ItemQuery<Sample> query = createQuery();
     query.restrict(
       Restrictions.in(
@@ -73 +81 @@
       )
     );
-    query.setParameter("biosources", bioSources, null);
+    query.setParameter("biosources", sourceIds, Type.INT);
     int size = samples.size();
     samples.addAll(query.list(dc));
     return samples.size() - size;
   }
+  // -------------------------------------------------
+  
+  /**
+    Create a query for loading samples. The default implemenation will
+    simply load all samples. The restriction needed to locate the biosources
+    that are parents is automatically applied by the <code>transform</code>
+    method. Subclasses may override this method to create an alternate query
+    (for example, with more filters).
+    @return A query object
+  */
+  protected ItemQuery<Sample> createQuery()
+  {
+    ItemQuery<Sample> query = Sample.getQuery();
+    query.include(Include.ALL);
+    return query;
+  }
   
 }

trunk/src/core/net/sf/basedb/util/biomaterial/ListUtil.java

@@ -22 +22 @@
 package net.sf.basedb.util.biomaterial;
 
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashSet;
-import java.util.Set;
-
+import java.util.Iterator;
+import java.util.List;
+
+import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BioMaterial;
 import net.sf.basedb.core.BioMaterialList;
+import net.sf.basedb.core.BioSource;
+import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.Extract;
 import net.sf.basedb.core.InvalidDataException;
+import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.LabeledExtract;
 import net.sf.basedb.core.PermissionDeniedException;
+import net.sf.basedb.core.Sample;
+import net.sf.basedb.util.collections.AddAllTransformer;
 import net.sf.basedb.util.collections.CollectionTransformer;
+import net.sf.basedb.util.collections.MultiStepCollectionTransformer;
 
 /**
@@ -43 +56 @@
 
   /**
+    Get a query that returns all biomaterials that can possibly be 
+    members of this list. NOTE! This is just a convenience function
+    that calls {@link BioSource#getQuery()}, etc. depending on the
+    member type of the list.
+    @return An {@link ItemQuery} object
+    @throws BaseException If the query could not be created and configured.
+  */
+  public static ItemQuery<? extends BioMaterial> getQuery(Item biomaterialType)
+    throws BaseException
+  {
+    ItemQuery<? extends BioMaterial> query;
+    if (biomaterialType == Item.BIOSOURCE)
+    {
+      query = BioSource.getQuery();
+    }
+    else if (biomaterialType == Item.SAMPLE)
+    {
+      query = Sample.getQuery();
+    }
+    else if (biomaterialType == Item.EXTRACT)
+    {
+      query = Extract.getQuery();
+    }
+    else if (biomaterialType == Item.LABELEDEXTRACT)
+    {
+      query = LabeledExtract.getQuery();
+    }
+    else
+    {
+      throw new AssertionError("Can't create query for item type: " + 
+          biomaterialType);
+    }
+    return query;
+  }
+  
+  
+  /**
     Adds items to a biomaterial list. The source collection can optionally
-    be transformed by a transformer. If not transformer is given, the
+    be transformed by a transformer. If no transformer is given, the
     source collection is added. The items added to the list must of course
     be of the correct {@link BioMaterialList#getMemberType()} for the list.
     
     @param list The list to add items to
-    @param source The source collection of biomaterials
+    @param sources The source collection of biomaterials
     @param transformer An optional transformer
     @return The number of items added to the biomaterial list
@@ -58 +108 @@
   */
   public static <S extends BioMaterial> int addToList(BioMaterialList list, 
-    Collection<? extends S> source, 
+    Collection<? extends S> sources, 
     CollectionTransformer<S, ? extends BioMaterial> transformer)
     throws InvalidDataException, PermissionDeniedException
   {
-    Set<BioMaterial> toAdd = new HashSet<BioMaterial>();
-    if (transformer == null)
-    {
-      toAdd.addAll(source);
+    Iterator<? extends BioMaterial> iterator = null;
+    if (transformer != null)
+    {
+      Collection<BioMaterial> transformed = new HashSet<BioMaterial>();
+      transformer.transform(sources, transformed);
+      iterator = transformed.iterator();
     }
     else
     {
-      toAdd = new HashSet<BioMaterial>();
-      transformer.transform(source, toAdd);
-    }
-    int added = list.add(toAdd.iterator());
+      iterator = sources.iterator();
+    }
+    int added = list.add(iterator);
     return added;
   }
+  
+  /**
+    Create a transformer that can transform a collection with
+    <code>sourceItem</code>:s into a collection with <code>destinationItem</code>:s
+    by following parent/child paths. Both the source and destination must be
+    one of {@link Item#BIOSOURCE}, {@link Item#SAMPLE}, {@link Item#EXTRACT}
+    or {@link Item#LABELEDEXTRACT}.
+    
+    @param dc The DbControl the transformers should use for loading
+      items from the database
+    @param sourceItem The type of source items
+    @param destinationItem The type of destination items
+    @param pooled If pooled children/parents should be considered or not
+    @return A collection transformer (never null)
+  */
+  @SuppressWarnings("unchecked")
+  public static CollectionTransformer createTransformer(DbControl dc, Item sourceItem, Item destinationItem, boolean pooled)
+  {
+    // The allowed item types
+    final List<Item> INDEX = Arrays.asList(new Item[] { Item.BIOSOURCE, Item.SAMPLE, Item.EXTRACT, Item.LABELEDEXTRACT });
+    int dIndex = INDEX.indexOf(destinationItem);
+    if (dIndex == -1) 
+    {
+      throw new InvalidDataException("Destination item type must be a biomaterial: " + 
+          destinationItem);
+    }
+    int sIndex = INDEX.indexOf(sourceItem);
+    if (dIndex == -1) 
+    {
+      throw new InvalidDataException("Source item type must be a biomaterial: " + 
+          destinationItem);
+    }
+    int step = sIndex < dIndex ? 1 : -1;
+    
+    List<CollectionTransformer> transformers = new ArrayList<CollectionTransformer>();
+    while (sIndex != dIndex)
+    {
+      if (sourceItem == Item.BIOSOURCE)
+      {
+        // Moving down
+        transformers.add(new BioSourceToSampleTransformer(dc));
+      }
+      else if (sourceItem == Item.SAMPLE)
+      {
+        if (step == 1)
+        {
+          // Moving down
+          if (pooled) transformers.add(new PooledChildrenTransformer<Sample>(dc, true, Sample.getQuery()));
+          transformers.add(new SampleToExtractTransformer(dc));
+        }
+        else
+        {
+          // Moving up
+          if (pooled) transformers.add(new PooledParentsTransformer<Sample>(dc, true, Sample.getQuery()));
+          transformers.add(new SampleToBioSourceTransformer(dc));
+        }
+      }
+      else if (sourceItem == Item.EXTRACT)
+      {
+        if (step == 1)
+        {
+          // Moving down
+          if (pooled) transformers.add(new PooledChildrenTransformer<Extract>(dc, true, Extract.getQuery()));
+          transformers.add(new ExtractToLabeledExtractTransformer(dc));
+        }
+        else
+        {
+          // Moving up
+          if (pooled) transformers.add(new PooledParentsTransformer<Extract>(dc, true, Extract.getQuery()));
+          transformers.add(new ExtractToSampleTransformer(dc));
+        }
+      }
+      else if (sourceItem == Item.LABELEDEXTRACT)
+      {
+        // Moving up
+        if (pooled) transformers.add(new PooledParentsTransformer<LabeledExtract>(dc, true, LabeledExtract.getQuery()));
+        transformers.add(new LabeledExtractToExtractTransformer(dc));
+      }
+      sIndex += step;
+      sourceItem = INDEX.get(sIndex);
+    }
+    
+    if (transformers.size() == 0)
+    {
+      // When sourceItem == destinationItem to begin with
+      transformers.add(new AddAllTransformer());
+    }
+    
+    if (pooled && destinationItem != Item.BIOSOURCE)
+    {
+      if (step == 1)
+      {
+        // Moving down
+        transformers.add(new PooledChildrenTransformer(dc, true, getQuery(destinationItem)));
+      }
+      else
+      {
+        // Moving up
+        transformers.add(new PooledParentsTransformer(dc, true, getQuery(destinationItem)));
+      }
+    }
+    
+    CollectionTransformer ct = null;
+    if (transformers.size() == 1)
+    {
+      ct = transformers.get(0);
+    }
+    else
+    {
+      ct = new MultiStepCollectionTransformer(transformers);
+    }
+    return ct;
+  }
+  
 }

trunk/src/core/net/sf/basedb/util/biomaterial/PooledChildrenTransformer.java

@@ -52 +52 @@
   private final DbControl dc;
   private final ItemQuery<I> query;
-  public PooledChildrenTransformer(DbControl dc, ItemQuery<I> query)
+  private final boolean copySources;
+  
+  public PooledChildrenTransformer(DbControl dc, boolean copySources, ItemQuery<I> query)
   {
     this.dc = dc;
+    this.copySources = copySources;
     this.query = query;
     query.include(Include.ALL);
@@ -84 +87 @@
     int originalSize = destination.size();
     
+    // Copy source biomaterials
+    if (copySources) destination.addAll(source);
+    
     // We need to loop so we can move down as many levels as we need
     while (sourceIds.size() > 0)
@@ -98 +104 @@
     return destination.size() - originalSize;
   }
+  // --------------------------------------------------
 
 }

trunk/src/core/net/sf/basedb/util/collections/CollectionTransformer.java

@@ -31 +31 @@
   should NOT use the same collection as both source and destination since that
   may interfere with iterators on the source collection. 
-  The destinatio collection may contain elements of the same or a different type
+  The destination collection may contain elements of the same or a different type
   as the source collection.
 
@@ -51 +51 @@
       This value may have a different meaning depending on the implementor. For
       example, some implementor may add elements while other implementor may 
-      remove elements. A return value of 0, indicates that no modifications at all
+      remove elements. A return value of 0 should always indicate that no modifications 
       has been made to the destination collection.
   */

trunk/src/test/TestSample.java

@@ -446 +446 @@
       dc = TestUtil.getDbControl();
       Sample s = Sample.getById(dc, sampleId);
-      PooledChildrenTransformer<Sample> pct = new PooledChildrenTransformer<Sample>(dc, Sample.getQuery());
+      PooledChildrenTransformer<Sample> pct = new PooledChildrenTransformer<Sample>(dc, false, Sample.getQuery());
       List<Sample> children = new ArrayList<Sample>();
       int numAdded = pct.transform(Collections.singleton(s), children);

trunk/www/biomaterials/lists/edit_list.jsp

@@ -54 +54 @@
   int numSelectedLists = cc.getSelected().size();
   String formId = request.getParameter("formId");
-  String fromContext = Values.getString(request.getParameter("fromContext"));
+  String fromContext = Values.getStringOrNull(request.getParameter("fromContext"));
   String subContext = request.getParameter("subContext");
 
@@ -62 +62 @@
     cc.removeObject("item");
     addBioMaterials = Values.getBoolean(request.getParameter("addBioMaterials"));
-    memberType = fromContext != null ? Item.valueOf(fromContext) : Item.fromValue(Values.getInt(cc.getPropertyValue("memberType")));
+    if (numSelectedLists > 0)
+    {
+      for (int selectedId : cc.getSelected())
+      {
+        BioMaterialList selectedList = BioMaterialList.getById(dc, selectedId);
+        if (memberType == null)
+        {
+          memberType = selectedList.getMemberType();
+        }
+        else if (memberType != selectedList.getMemberType())
+        {
+          numSelectedLists = 0;
+          memberType = null;
+          break;
+        }
+      }
+    }
+    if (memberType == null)
+    {
+      memberType = fromContext != null ? Item.valueOf(fromContext) : Item.fromValue(Values.getInt(cc.getPropertyValue("memberType")));
+    }
     mergeLists = numSelectedLists > 0;
   }
@@ -138 +158 @@
       Forms.checkRadio(radio, name);
     }
-    function setAddToList(memberType, selectedOption)
-    {
-      var frm = document.forms['list'];
-      if (memberType)
-      {
-        Forms.selectListOption(frm.memberType, memberType);
-      }
-      if (selectedOption)
-      {
-        Forms.checkRadio(frm.add, selectedOption);
-      }
-    }
+
     // Get the ID:s of all selected items
     var selectedItems = new Array();
@@ -199 +208 @@
         <td class="prompt">Member type</td>
         <td>
-          <select name="memberType" <%=fromContext != null ? "disabled" : ""%>>
+          <select name="memberType" <%=mergeLists ? "disabled" : "" %>>
             <option value="BIOSOURCE" <%=memberType == Item.BIOSOURCE ? "selected" : ""%>>Biosource
             <option value="SAMPLE" <%=memberType == Item.SAMPLE ? "selected" : ""%>>Sample
@@ -210 +219 @@
       if (addBioMaterials)
       {
-        boolean hasSourceOption = true;
-        boolean hasPooledOption = true;
-        boolean hasChildOption = true;
-        Item childType = null;
-        if (memberType == Item.BIOSOURCE)
-        {
-          hasPooledOption = false;
-          childType = Item.SAMPLE;
-        }
-        else if (memberType == Item.SAMPLE)
-        {
-          childType = Item.EXTRACT;
-        }
-        else if (memberType == Item.EXTRACT)
-        {
-          childType = Item.LABELEDEXTRACT;
-        }
-        else if (memberType == Item.LABELEDEXTRACT)
-        {
-          hasChildOption = false;
-        }
         %>
         <tr valign="top">
@@ -248 +236 @@
         </tr>
         <tr>
-          <td class="prompt">Add to list</td>
+          <td class="prompt">Include pooled</td>
           <td>
-            <%
-            if (hasSourceOption)
-            {
-              %>
-              <input type="radio" name="add" value="source" checked
-                onchange="setAddToList('<%=memberType.name()%>')"><a 
-                href="javascript:setAddToList('<%=memberType.name()%>', 'source');"
-                >Source items only</a><br>
-              <%
-            }
-            if (hasPooledOption)
-            {
-              %>
-              <input type="radio" name="add" value="pooled"
-                onchange="setAddToList('<%=memberType.name()%>')"><a 
-                href="javascript:setAddToList('<%=memberType.name()%>', 'pooled');"
-                >Source items + pooled children of same type (<%=memberType%>)</a><br>
-              <%
-            }
-            if (hasChildOption)
-            {
-              %>
-              <input type="radio" name="add" value="children"
-                onchange="setAddToList('<%=childType.name()%>')"><a 
-                href="javascript:setAddToList('<%=childType.name()%>', 'children');"
-                >Children of next type (<%=childType%>)</a><br>
-              <%  
-            }
-            %>
+            <input type="checkbox" name="pooled" value="1" ><a 
+                href="javascript:Forms.toggleCheckbox(document.forms['list'].pooled);"
+                >Include pooled children/parents in the list</a><br>
           </td>
         </tr>

trunk/www/biomaterials/lists/index.jsp

@@ -47 +47 @@
   import="net.sf.basedb.util.OwnableUtil"
   import="net.sf.basedb.util.biomaterial.BioSourceToSampleTransformer"
+  import="net.sf.basedb.util.biomaterial.SampleToExtractTransformer"
+  import="net.sf.basedb.util.biomaterial.ExtractToLabeledExtractTransformer"
   import="net.sf.basedb.util.biomaterial.PooledChildrenTransformer"
   import="net.sf.basedb.util.collections.CollectionTransformer"
@@ -151 +153 @@
         Item fromContext = Item.valueOf(request.getParameter("fromContext"));
         String subContext = Values.getString(request.getParameter("subContext"), "");
+        boolean pooled = Values.getBoolean(request.getParameter("pooled"));
+        
         ItemQuery<? extends BioMaterial> query = 
           (ItemQuery<? extends BioMaterial>)sc.getCurrentContext(fromContext, subContext).getQuery();
@@ -172 +176 @@
         }
         // else -- no modifications to the query mean that we only get the current page
+        
+        // This is our list of source items (eg. the selected items in the list)
         List<? extends BioMaterial> sources = query.list(dc);
-        CollectionTransformer transformer = null;
-        if ("source".equals(add))
-        {
-          // No transformer needed
-        }
-        else if ("pooled".equals(add))
-        {
-          ListUtil.addToList(list, sources, null);
-          ItemQuery<? extends BioMaterial> pooledQuery = list.getAllBioMaterials();
-          transformer = new PooledChildrenTransformer(dc, pooledQuery);
-        }
-        else if ("children".equals(add))
-        {
-          if (memberType == Item.SAMPLE)
-          {
-            transformer = new BioSourceToSampleTransformer(dc);
-          }
-          // TODO -- other biomaterial types
-        }
-        ListUtil.addToList(list, sources, transformer);
+        // Create a transformer that takes the source list and finds related
+        // items
+        CollectionTransformer transformer = 
+          ListUtil.createTransformer(dc, fromContext, memberType, pooled);
+        int numAdded = ListUtil.addToList(list, sources, transformer);
       }